Development of Chimeric Molecules That Degrade the Estrogen Receptor Using Decoy Oligonucleotide Ligands

Abstract

Targeted protein degradation using chimeric small molecules, such as proteolysis-targeting chimeras (PROTACs) and specific and nongenetic inhibitors of apoptosis protein (IAP)-dependent protein erasers (SNIPERs), has attracted attention as a method for degrading intracellular target proteins via the ubiquitin-proteasome system (UPS). These chimeric molecules target a variety of proteins using small molecules that can bind to the proteins. However, it is difficult to develop such degraders in the absence of suitable small-molecule ligands for the target proteins, such as for transcription factors (TFs). Therefore, we constructed the chimeric molecule LCL-ER­(dec), which consists of a decoy oligonucleotide that can bind to estrogen receptor α (ERα) and an IAP ligand, LCL161 (LCL), in a click reaction. LCL-ER­(dec) was found to selectively degrade ERα via the UPS. These findings will be applicable to the development of other oligonucleotide-type degraders that target different TFs.

PROTAC Degrader of Estrogen Receptor α Targeting DNA-Binding Domain in Breast Cancer

“…23,24 Based on TF-PROTACs, decoy-based chimeric degraders have been developed, which can involve different kinds of E3 ligands. 25 Moreover, G4-PROTAC and aptamer-PROTAC were raised as novel strategies to target proteins because G-quadruplexes and aptamers can serve as high-quality warheads. 26,27 Overall, these works fully illustrate the feasibility of DNA-based PROTACs.…”

“…For instance, TRAFTAC was the first DNA-based PROTAC proposed by the Craws group, which provides a generalizable strategy for targeted transcription factor degradation requiring the ectopic expression of Cas-9 protein in the cell based on CRISPR technology . Subsequently, two other DNA-based PROTACs, namely, TF-PROTACs and O PROTACs, were developed, which can directly recruit transcription factors and E3 enzymes to achieve the degradation of target proteins. , Based on TF-PROTACs, decoy-based chimeric degraders have been developed, which can involve different kinds of E3 ligands . Moreover, G4-PROTAC and aptamer-PROTAC were raised as novel strategies to target proteins because G-quadruplexes and aptamers can serve as high-quality warheads. , Overall, these works fully illustrate the feasibility of DNA-based PROTACs.…”

“…Most of the currently approved drugs and the existing ERα PROTACs concentrate on the LBD of ERα, the main cause of drug resistance . It is pertinent to note that ERα is a transcription factor consisting of a DNA-binding domain. , Thus, in this work, we designed an ERE-PROTAC via a click reaction, selecting the DBD of ERα as the target of PROTAC and estrogen response element (ERE) as a recognized unit of PROTAC, a DNA sequence in cells that binds with the DBD of ERα in the nanomolar range. , The 5′-terminus of the sense sequence of ERE (ssERE), which was modified with an azide group (named N 3 -ssERE), and VH032, which was modified with a terminal alkyne (VH032-propargyl), were linked by the copper-catalyzed azide–alkyne cycloaddition (CUAAC) reaction to form ERE-PROTAC (Figure B). Specifically, the ERE sequence recruited ERα, while the typical small molecule VH032 recruited the endogenous von Hippel–Lindau (VHL) E3 ligase. − The designed ERE-PROTAC can induce the ubiquitination of ERα, which is subsequently degraded by the proteasome (Figure C).…”

Enriching Proteolysis Targeting Chimeras with a Second Modality: When Two Are Better Than One

“…Interestingly, a similar approach was recently exploited to develop PROTACs that degrade the estrogen receptor using decoy oligonucleotide ligands . Beside belonging to the nuclear hormone receptor superfamily, ERα can also act as a TF, forming transcriptional complexes on the DNA response sequence, thereby regulating gene expression.…”

“…Interestingly, a similar approach was recently exploited to develop PROTACs that degrade the estrogen receptor using decoy oligonucleotide ligands. 137 Beside belonging to the nuclear hormone receptor superfamily, ERα can also act as a TF, forming transcriptional complexes on the DNA response sequence, thereby regulating gene expression. The developed decoy oligonucleotide is a double-stranded decoy, namely LCL-ER(dec) (49), designed from the sequence of the estrogenresponsive element that is known to tightly bind ERα.…”